Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nt2b- -------------CCEECCCCEECCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH-----CHHHHHHHHHHHHHHHHHHHH-------------HCCCCHHHHHC----CCCCC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHHCCCCCC---------------CCHHHHCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHCC------ >P1;d2ozbb1 ------------------------------CCCCHHHHHH---------HHHHHHH----HHHHHHHHHHHHHHHHHCCCCCCHHHHCCC-HHHHHHHHHHH-CCCHHHCCCCCCHHHCCCHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHCCCHHHHCCCCCCC----------CCCCCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHCC-- >P1;d3nvia- ------------------------------CCCCHHHHHH---------HHHHHHH----HHHHHHHHHHHHHHHHHHHHCCCHHHHCCC-HHHHHHHHHHC-CC-HHHCCHHHHHCCCCCHHHHHCCHHHHHCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHHHHCCCHHHHHHHHHCCCCCCCCCHHHHCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHHHHHHHHHHHCC >P1;d5ganf2 CCCCCCCHHHHHHHCCCCCCCCC--CCCCHHHHCCHHHHHHCCCCCCC-HHHHHHH----HHHHHHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHH-CCHHHHHHHHHHHCHHHHHHCC-CCHHHHHHHHCCC-CCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC-- PSA >P1;d1nt2b- -------------76210000423684822bb323112023319791626347105901a970861376045306633760285-----740450181055057136407-------------64466066527----9763a----7058334705635762651174046105800000040070530010001060035015063840161066---------------90102615005605896153006200410210030001217--50950453056316618------ >P1;d2ozbb1 ------------------------------baa4424700---------7105614----715650671164037305410330582077-43300400410-42608506a18803710686407601820983827-706a82375068105502711432762385057306810100110070310020004051186017353760241337c----------76680030040b1037047a2244006100510050043008-7736a0830661474047408914c-- >P1;d3nvia- ------------------------------9776315500---------8105405----814840783075017302700230581066-44300400350-01-17606684059180987308402412760818-606a8505603620350371255277235405700570020022008040002001307005500416494011012493255257775a515202046163048058602320060004000500420254675----20770376055407724776 >P1;d5ganf2 88930400830560638380a42--703107700303711779a3127-5025004----2047007202500361049205-0282003223003003000548827b--5050463066680981074041294166871a69833207402600403502-6038203730761010014004-6200500140110-7018354870040229750a45a4b6a07084030260-00461569004400720052004004201a3a878527405613740454066348-- Translating the sequences -------------*****************CCC*HHHHHH**********HHHHHH******HHHHHHHHHHHHHHH******H-----C*HHHHHHHHHHH****HHH*-------------H**C*HHHHHC----*CCC*----*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHHCCCCCC---------------CCHHHHCHHHHCCC****HHHHHHHHHHHHHHHHHHHHCCC--CC*HHHHHHHHHHHH**------ ------------------------------CCCCHHHHHH---------HHHHHHH----HHHHHHHHHHHHHHHHH***CC*H***CCC-HHHHHHHHHHH-CC*HHH******H*******H****HHHHHCCCCC-CCC******HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH*HHHHHHHHHHHCCHHHHHCCCHHHHCCCCCC*----------CCCCCC****CHHHHCCC***HHHHHHHHHHHHHHHHHHHH*-CCC*CC*HHHHHHHHHHHHHHHH**-- ------------------------------CCCCHHHHHH---------HHHHHHH----HHHHHHHHHHHHHHHHH***CC*H***CCC-HHHHHHHHHH*-CC-HHH******H*******H**C*HHHHHCCCCC-CCC******HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHH**CCC************CCCCCCHHHHCHHHHCCC***HHHHHHHHHHHHHHHHHHHHHCCCC----*HHHHHHHHHHHHHHH**** ***********************--********C*HHHHH********-HHHHHHH----HHHHHHHHHHHHHHHHH***CC-****CCC*HHHHHHHHHHH*CC****--****H**********C*HHH**CCCCC*CCC*******HHHHHHH**HHHHH-**HHHHHHHHHHHCHHHHHH*C-**HHHHHHHHCC*-***CCCHHHHCCCCCC***********CCCCCCHHHHC-***CCC***HHHHHHHHHHHHHHHHHHHHHCCCC*CC*HHHHHHHHHHHHHHHH**-- 89124.tem _________________________________ -------------**********--*****CCCCHHHHHH********-HHHHHHH----HHHHHHHHHHHHHHHHH***CC*H***CCC*HHHHHHHHHHH*CC*HHH******H*******H**C*HHHHHCCCCC*CCC******HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCHHHHHHHHHHHCCHHHHHCCCHHHHCCCCCC***********CCCCCCHHHHCHHHHCCC***HHHHHHHHHHHHHHHHHHHHHCCCC*CC*HHHHHHHHHHHHHHHH**-- Structural block scores 0 12 - 4.3 M 75.0 75.0 75.0 4.2 13 22 * 3.5 M 2.2 75.0 75.0 4.5 23 24 - 4.3 M 4.5 75.0 75.0 75.0 25 29 * 3.5 M 4.8 75.0 75.0 2.2 30 33 C 4.3 M 7.0 9.1 7.2 3.5 34 39 H 4.9 H 1.5 2.8 2.3 2.5 40 47 * 3.5 M 4.9 75.0 75.0 5.8 49 55 H 4.9 H 3.7 3.4 3.3 2.3 56 59 - 4.3 M 5.1 75.0 75.0 75.0 60 76 H 4.9 H 4.4 3.6 3.9 2.3 77 79 * 1.0 P 5.3 3.3 3.0 5.0 80 81 C 4.3 M 1.0 1.5 1.0 2.5 84 86 * 2.3 P 75.0 5.0 4.7 4.0 87 89 C 4.5 M 52.3 4.7 4.0 1.0 91 101 H 4.9 H 2.6 1.7 2.1 1.0 103 104 C 4.3 M 4.0 3.0 0.5 6.0 106 108 H 4.3 M 3.3 4.3 4.7 6.8 109 114 * 2.5 P 63.7 5.6 4.0 26.7 116 122 * 2.3 P 75.0 4.4 6.0 5.0 124 125 * 1.0 P 4.0 3.5 4.0 8.5 128 132 H 4.7 H 3.8 4.0 3.2 3.2 133 137 C 4.4 M 61.4 5.6 4.6 4.4 139 141 C 5.0 H 5.3 4.3 4.0 5.3 142 147 * 1.9 P 52.9 5.9 5.8 6.6 148 176 H 4.9 H 3.9 3.7 3.3 5.4 178 184 H 4.9 H 0.6 0.4 0.9 0.9 186 196 H 4.8 H 0.9 0.9 0.9 8.5 197 198 C 5.0 H 3.0 3.0 3.5 1.0 199 203 H 4.3 M 1.8 3.2 2.0 16.6 204 206 C 5.0 H 3.7 5.0 3.7 5.3 207 210 H 5.0 H 3.8 4.0 4.2 4.8 211 216 C 4.7 H 3.3 3.3 1.5 2.8 217 227 * 3.4 M 75.0 69.3 5.2 6.7 228 233 C 4.5 M 51.5 4.5 3.9 3.2 234 237 H 4.3 M 2.2 1.8 3.0 2.8 239 242 H 4.3 M 2.5 3.9 3.2 19.8 243 245 C 5.0 H 3.7 3.7 4.3 4.0 246 248 * 1.0 P 7.7 6.5 4.7 5.0 249 269 H 4.9 H 1.4 2.0 1.7 2.2 270 273 C 4.7 H 21.2 23.0 5.5 7.1 275 276 C 4.3 M 2.5 5.2 75.0 3.5 278 293 H 4.8 H 12.7 4.0 3.9 3.6 294 295 * 2.3 P 75.0 8.2 5.5 6.0 296 297 - 4.3 M 75.0 75.0 6.5 75.0 >>>>>>